How to: Extracting EMIT Spectra using a Shapefile/GeoJSON¶

Summary

In this notebook we will open a netCDF4 file from the Earth Surface Minteral Dust Source Investigation (EMIT) as an xarray.Dataset. We will then extract extract or clip to an area using a .geojson file (will also work with shapefile). The workflows outlined here will work with reflectance L2A or radiance L1B data.

Requirements:

  • A NASA Earthdata Login account is required to download EMIT data
  • Selected the emit_tutorials environment as the kernel for this notebook.
    • For instructions on setting up the environment, follow the instructions in the Prerequisites section of the README.md included in the repository.
  • Downloaded the necessary EMIT files to the ../data/ folder.
    • For download instructions see the Prerequisites section of the README.md included in the repository.

Learning Objectives

  • How to open and EMIT Dataset as an xarray.Dataset
  • How to extract values or clip an EMIT dataset to a region of interest
  • How to write a new netCDF4 output using the clipped data

Setup¶

Import the required Python libraries.

In [1]:
# Import Packages
import os
from osgeo import gdal
import xarray as xr
import rasterio as rio
import rioxarray as rxr
import hvplot.xarray
import holoviews as hv
import geopandas as gp
import sys
sys.path.append('../modules/')
from emit_tools import emit_xarray

Set the path to the downloaded EMIT data as an object. In this example we use an L2A Reflectance file.

In [2]:
fp = '../data/EMIT_L2A_RFL_001_20220903T163129_2224611_012.nc'

Open the file downloaded and defined as fp. To do this, we will use the emit_xarray function from the emit_tools module. This module contains a few helpful functions that can be used with EMIT data.

In [3]:
ds = emit_xarray(fp)
ds
Out[3]:
<xarray.Dataset>
Dimensions:      (latitude: 2009, longitude: 2353, bands: 285)
Coordinates:
  * latitude     (latitude) float64 -39.31 -39.31 -39.31 ... -40.39 -40.4 -40.4
  * longitude    (longitude) float64 -62.51 -62.51 -62.51 ... -61.24 -61.24
    wavelengths  (bands) float32 381.0 388.4 395.8 ... 2.486e+03 2.493e+03
    fwhm         (bands) float32 8.415 8.415 8.415 8.415 ... 8.806 8.807 8.809
    spatial_ref  int32 0
Dimensions without coordinates: bands
Data variables:
    reflectance  (latitude, longitude, bands) float32 nan nan nan ... nan nan
Attributes: (12/38)
    ncei_template_version:             NCEI_NetCDF_Swath_Template_v2.0
    summary:                           The Earth Surface Mineral Dust Source ...
    keywords:                          Imaging Spectroscopy, minerals, EMIT, ...
    Conventions:                       CF-1.63
    sensor:                            EMIT (Earth Surface Mineral Dust Sourc...
    instrument:                        EMIT
    ...                                ...
    southernmost_latitude:             -40.39610428069674
    spatialResolution:                 0.000542232520256367
    spatial_ref:                       GEOGCS["WGS 84",DATUM["WGS_1984",SPHER...
    geotransform:                      [-6.25120945e+01  5.42232520e-04 -0.00...
    day_night_flag:                    Day
    title:                             EMIT L2A Surface Reflectance 60 m V001
xarray.Dataset
    • latitude: 2009
    • longitude: 2353
    • bands: 285
    • latitude
      (latitude)
      float64
      -39.31 -39.31 ... -40.4 -40.4
      long_name :
      Latitude (WGS-84)
      units :
      degrees north
      array([-39.306759, -39.307301, -39.307844, ..., -40.394478, -40.39502 ,
       -40.395562])
    • longitude
      (longitude)
      float64
      -62.51 -62.51 ... -61.24 -61.24
      long_name :
      Longitude (WGS-84)
      units :
      degrees east
      array([-62.512095, -62.511552, -62.51101 , ..., -61.237848, -61.237306,
       -61.236764])
    • wavelengths
      (bands)
      float32
      381.0 388.4 ... 2.486e+03 2.493e+03
      long_name :
      Wavelength Centers
      units :
      nm
      array([ 381.00558,  388.4092 ,  395.81583,  403.2254 ,  410.638  ,
        418.0536 ,  425.47214,  432.8927 ,  440.31726,  447.7428 ,
        455.17035,  462.59888,  470.0304 ,  477.46292,  484.89743,
        492.33292,  499.77142,  507.2099 ,  514.6504 ,  522.0909 ,
        529.5333 ,  536.9768 ,  544.42126,  551.8667 ,  559.3142 ,
        566.7616 ,  574.20905,  581.6585 ,  589.108  ,  596.55835,
        604.0098 ,  611.4622 ,  618.9146 ,  626.36804,  633.8215 ,
        641.2759 ,  648.7303 ,  656.1857 ,  663.6411 ,  671.09753,
        678.5539 ,  686.0103 ,  693.4677 ,  700.9251 ,  708.38354,
        715.84094,  723.2993 ,  730.7587 ,  738.2171 ,  745.6765 ,
        753.1359 ,  760.5963 ,  768.0557 ,  775.5161 ,  782.97754,
        790.4379 ,  797.89935,  805.36176,  812.8232 ,  820.2846 ,
        827.746  ,  835.2074 ,  842.66986,  850.1313 ,  857.5937 ,
        865.0551 ,  872.5176 ,  879.98004,  887.44147,  894.90393,
        902.3664 ,  909.82886,  917.2913 ,  924.7538 ,  932.21625,
        939.6788 ,  947.14026,  954.6027 ,  962.0643 ,  969.5268 ,
        976.9883 ,  984.4498 ,  991.9114 ,  999.37286, 1006.8344 ,
       1014.295  , 1021.7566 , 1029.2172 , 1036.6777 , 1044.1383 ,
       1051.5989 , 1059.0596 , 1066.5201 , 1073.9797 , 1081.4404 ,
       1088.9    , 1096.3597 , 1103.8184 , 1111.2781 , 1118.7368 ,
...
       1796.4385 , 1803.8701 , 1811.3008 , 1818.7314 , 1826.1611 ,
       1833.591  , 1841.0206 , 1848.4495 , 1855.8773 , 1863.3052 ,
       1870.733  , 1878.16   , 1885.5869 , 1893.013  , 1900.439  ,
       1907.864  , 1915.2892 , 1922.7133 , 1930.1375 , 1937.5607 ,
       1944.9839 , 1952.4071 , 1959.8295 , 1967.2518 , 1974.6732 ,
       1982.0946 , 1989.515  , 1996.9355 , 2004.355  , 2011.7745 ,
       2019.1931 , 2026.6118 , 2034.0304 , 2041.4471 , 2048.865  ,
       2056.2808 , 2063.6965 , 2071.1123 , 2078.5273 , 2085.9421 ,
       2093.3562 , 2100.769  , 2108.1821 , 2115.5942 , 2123.0063 ,
       2130.4175 , 2137.8289 , 2145.239  , 2152.6482 , 2160.0576 ,
       2167.467  , 2174.8755 , 2182.283  , 2189.6904 , 2197.097  ,
       2204.5034 , 2211.9092 , 2219.3147 , 2226.7195 , 2234.1233 ,
       2241.5269 , 2248.9297 , 2256.3328 , 2263.7346 , 2271.1365 ,
       2278.5376 , 2285.9387 , 2293.3386 , 2300.7378 , 2308.136  ,
       2315.5342 , 2322.9326 , 2330.3298 , 2337.7263 , 2345.1216 ,
       2352.517  , 2359.9126 , 2367.3071 , 2374.7007 , 2382.0935 ,
       2389.486  , 2396.878  , 2404.2695 , 2411.6604 , 2419.0513 ,
       2426.4402 , 2433.8303 , 2441.2183 , 2448.6064 , 2455.9944 ,
       2463.3816 , 2470.7678 , 2478.153  , 2485.5386 , 2492.9238 ],
      dtype=float32)
    • fwhm
      (bands)
      float32
      8.415 8.415 8.415 ... 8.807 8.809
      long_name :
      Full Width at Half Max
      units :
      nm
      array([8.415, 8.415, 8.415, 8.415, 8.417, 8.418, 8.419, 8.421, 8.422,
       8.424, 8.425, 8.426, 8.428, 8.429, 8.431, 8.432, 8.433, 8.435,
       8.436, 8.438, 8.439, 8.44 , 8.442, 8.443, 8.445, 8.446, 8.447,
       8.449, 8.45 , 8.452, 8.453, 8.454, 8.456, 8.457, 8.459, 8.46 ,
       8.461, 8.463, 8.464, 8.466, 8.467, 8.468, 8.47 , 8.471, 8.473,
       8.474, 8.475, 8.477, 8.478, 8.48 , 8.481, 8.482, 8.484, 8.485,
       8.487, 8.488, 8.489, 8.491, 8.492, 8.494, 8.495, 8.496, 8.498,
       8.499, 8.501, 8.502, 8.503, 8.505, 8.506, 8.508, 8.509, 8.51 ,
       8.512, 8.513, 8.515, 8.516, 8.517, 8.519, 8.52 , 8.522, 8.523,
       8.524, 8.526, 8.527, 8.529, 8.53 , 8.531, 8.533, 8.534, 8.536,
       8.537, 8.538, 8.54 , 8.541, 8.543, 8.544, 8.545, 8.547, 8.548,
       8.55 , 8.551, 8.552, 8.554, 8.555, 8.557, 8.558, 8.559, 8.561,
       8.562, 8.564, 8.565, 8.566, 8.568, 8.569, 8.571, 8.572, 8.573,
       8.575, 8.576, 8.578, 8.579, 8.58 , 8.582, 8.583, 8.585, 8.586,
       8.587, 8.589, 8.59 , 8.592, 8.593, 8.594, 8.596, 8.597, 8.599,
       8.6  , 8.601, 8.603, 8.604, 8.606, 8.607, 8.608, 8.61 , 8.611,
       8.613, 8.614, 8.615, 8.617, 8.618, 8.62 , 8.621, 8.622, 8.624,
       8.625, 8.627, 8.628, 8.629, 8.631, 8.632, 8.634, 8.635, 8.636,
       8.638, 8.639, 8.641, 8.642, 8.643, 8.645, 8.646, 8.648, 8.649,
       8.65 , 8.652, 8.653, 8.655, 8.656, 8.657, 8.659, 8.66 , 8.662,
       8.663, 8.664, 8.666, 8.667, 8.669, 8.67 , 8.671, 8.673, 8.674,
       8.676, 8.677, 8.678, 8.68 , 8.681, 8.683, 8.684, 8.685, 8.687,
       8.688, 8.69 , 8.691, 8.692, 8.694, 8.695, 8.697, 8.698, 8.699,
       8.701, 8.702, 8.704, 8.705, 8.706, 8.708, 8.709, 8.711, 8.712,
       8.714, 8.715, 8.716, 8.718, 8.719, 8.721, 8.722, 8.723, 8.725,
       8.726, 8.727, 8.729, 8.73 , 8.732, 8.733, 8.734, 8.736, 8.737,
       8.739, 8.74 , 8.741, 8.743, 8.744, 8.746, 8.747, 8.748, 8.75 ,
       8.751, 8.753, 8.754, 8.755, 8.757, 8.758, 8.76 , 8.761, 8.763,
       8.764, 8.765, 8.767, 8.768, 8.77 , 8.771, 8.772, 8.774, 8.775,
       8.777, 8.778, 8.779, 8.781, 8.782, 8.783, 8.785, 8.786, 8.788,
       8.789, 8.79 , 8.792, 8.793, 8.795, 8.796, 8.797, 8.799, 8.8  ,
       8.802, 8.803, 8.804, 8.806, 8.807, 8.809], dtype=float32)
    • spatial_ref
      ()
      int32
      0
      crs_wkt :
      GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
      semi_major_axis :
      6378137.0
      semi_minor_axis :
      6356752.314245179
      inverse_flattening :
      298.257223563
      reference_ellipsoid_name :
      WGS 84
      longitude_of_prime_meridian :
      0.0
      prime_meridian_name :
      Greenwich
      geographic_crs_name :
      WGS 84
      grid_mapping_name :
      latitude_longitude
      spatial_ref :
      GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
      array(0)
    • reflectance
      (latitude, longitude, bands)
      float32
      nan nan nan nan ... nan nan nan nan
      long_name :
      Surface Reflectance
      units :
      unitless
      array([[[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
...
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]]], dtype=float32)
    • latitude
      PandasIndex
      PandasIndex(Float64Index([  -39.3067591475017, -39.307301380021954, -39.307843612542214,
               -39.30838584506247,  -39.30892807758273,  -39.30947031010298,
               -39.31001254262324, -39.310554775143494, -39.311097007663754,
               -39.31163924018401,
              ...
               -40.39068195549418, -40.391224188014434, -40.391766420534694,
               -40.39230865305495,  -40.39285088557521,  -40.39339311809546,
               -40.39393535061572,  -40.39447758313597,  -40.39501981565623,
               -40.39556204817649],
             dtype='float64', name='latitude', length=2009))
    • longitude
      PandasIndex
      PandasIndex(Float64Index([  -62.5120945327963, -62.511552300276044, -62.511010067755784,
               -62.51046783523553,  -62.50992560271527,  -62.50938337019502,
               -62.50884113767476, -62.508298905154504, -62.507756672634244,
               -62.50721444011399,
              ...
               -61.24164373783563,  -61.24110150531537,  -61.24055927279512,
               -61.24001704027486, -61.239474807754604, -61.238932575234344,
               -61.23839034271409,  -61.23784811019384,  -61.23730587767358,
              -61.236763645153324],
             dtype='float64', name='longitude', length=2353))
  • ncei_template_version :
    NCEI_NetCDF_Swath_Template_v2.0
    summary :
    The Earth Surface Mineral Dust Source Investigation (EMIT) is an Earth Ventures-Instrument (EVI-4) Mission that maps the surface mineralogy of arid dust source regions via imaging spectroscopy in the visible and short-wave infrared (VSWIR). Installed on the International Space Station (ISS), the EMIT instrument is a Dyson imaging spectrometer that uses contiguous spectroscopic measurements from 410 to 2450 nm to resolve absoprtion features of iron oxides, clays, sulfates, carbonates, and other dust-forming minerals. During its one-year mission, EMIT will observe the sunlit Earth's dust source regions that occur within +/-52° latitude and produce maps of the source regions that can be used to improve forecasts of the role of mineral dust in the radiative forcing (warming or cooling) of the atmosphere.\n\nThis file contains L2A estimated surface reflectances and geolocation data. Reflectance estimates are created using an Optimal Estimation technique - see ATBD for details. Reflectance values are reported as fractions (relative to 1).
    keywords :
    Imaging Spectroscopy, minerals, EMIT, dust, radiative forcing
    Conventions :
    CF-1.63
    sensor :
    EMIT (Earth Surface Mineral Dust Source Investigation)
    instrument :
    EMIT
    platform :
    ISS
    processing_version :
    V1.0
    institution :
    NASA Jet Propulsion Laboratory/California Institute of Technology
    license :
    https://science.nasa.gov/earth-science/earth-science-data/data-information-policy/
    naming_authority :
    LPDAAC
    date_created :
    2022-11-14T09:50:54Z
    keywords_vocabulary :
    NASA Global Change Master Directory (GCMD) Science Keywords
    stdname_vocabulary :
    NetCDF Climate and Forecast (CF) Metadata Convention
    creator_name :
    Jet Propulsion Laboratory/California Institute of Technology
    creator_email :
    sarah.r.lundeen@jpl.nasa.gov
    creator_url :
    https://earth.jpl.nasa.gov/emit/
    project :
    Earth Surface Mineral Dust Source Investigation
    project_url :
    https://emit.jpl.nasa.gov/
    publisher_name :
    USGS LPDAAC
    publisher_url :
    https://lpdaac.usgs.gov
    publisher_email :
    lpdaac@usgs.gov
    identifier_product_doi_authority :
    https://doi.org
    flight_line :
    emit20220903t163129_o24611_s000
    time_coverage_start :
    2022-09-03T16:31:29+0000
    time_coverage_end :
    2022-09-03T16:31:41+0000
    software_build_version :
    010603
    product_version :
    01
    history :
    PGE Input files: radiance_file=/beegfs/store/emit/ops/data/acquisitions/20220903/emit20220903t163129/l1b/emit20220903t163129_o24611_s000_l1b_rdn_b0106_v01.img, pixel_locations_file=/beegfs/store/emit/ops/data/acquisitions/20220903/emit20220903t163129/l1b/emit20220903t163129_o24611_s000_l1b_loc_b0106_v01.img, observation_parameters_file=/beegfs/store/emit/ops/data/acquisitions/20220903/emit20220903t163129/l1b/emit20220903t163129_o24611_s000_l1b_obs_b0106_v01.img, surface_model_config=/beegfs/store/emit/ops/repos/emit-sds-l2a/surface/surface_20221020.json
    easternmost_longitude :
    -62.5120945327963
    northernmost_latitude :
    -39.3067591475017
    westernmost_longitude :
    -61.236221412633064
    southernmost_latitude :
    -40.39610428069674
    spatialResolution :
    0.000542232520256367
    spatial_ref :
    GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
    geotransform :
    [-6.25120945e+01 5.42232520e-04 -0.00000000e+00 -3.93067591e+01 -0.00000000e+00 -5.42232520e-04]
    day_night_flag :
    Day
    title :
    EMIT L2A Surface Reflectance 60 m V001

Using the read_file() function from geopandas, read in the .geojson file containing the polygon you wish to extract. If this cell results in an error, re-run it.

In [4]:
#import geopandas as gp
shape = gp.read_file('../data/isla_gaviota.geojson')
shape
Out[4]:
geometry
0 POLYGON ((-62.14758 -39.88951, -62.16900 -39.8...

Use the clip function from rasterio to clip the dataset to polygons from the geopandas.geodataframe. Setting all_touched to True will include pixels that intersected with the edges of the polygon.

In [6]:
clipped = ds.rio.clip(shape.geometry.values,shape.crs, all_touched=True)
clipped
Out[6]:
<xarray.Dataset>
Dimensions:      (latitude: 140, longitude: 163, bands: 285)
Coordinates:
  * latitude     (latitude) float64 -39.88 -39.88 -39.88 ... -39.95 -39.95
  * longitude    (longitude) float64 -62.2 -62.2 -62.2 ... -62.12 -62.12 -62.12
    wavelengths  (bands) float32 381.0 388.4 395.8 ... 2.486e+03 2.493e+03
    fwhm         (bands) float32 8.415 8.415 8.415 8.415 ... 8.806 8.807 8.809
    spatial_ref  int32 0
Dimensions without coordinates: bands
Data variables:
    reflectance  (latitude, longitude, bands) float32 nan nan nan ... nan nan
Attributes: (12/38)
    ncei_template_version:             NCEI_NetCDF_Swath_Template_v2.0
    summary:                           The Earth Surface Mineral Dust Source ...
    keywords:                          Imaging Spectroscopy, minerals, EMIT, ...
    Conventions:                       CF-1.63
    sensor:                            EMIT (Earth Surface Mineral Dust Sourc...
    instrument:                        EMIT
    ...                                ...
    southernmost_latitude:             -40.39610428069674
    spatialResolution:                 0.000542232520256367
    spatial_ref:                       GEOGCS["WGS 84",DATUM["WGS_1984",SPHER...
    geotransform:                      [-6.25120945e+01  5.42232520e-04 -0.00...
    day_night_flag:                    Day
    title:                             EMIT L2A Surface Reflectance 60 m V001
xarray.Dataset
    • latitude: 140
    • longitude: 163
    • bands: 285
    • latitude
      (latitude)
      float64
      -39.88 -39.88 ... -39.95 -39.95
      long_name :
      latitude
      units :
      degrees_north
      axis :
      Y
      standard_name :
      latitude
      array([-39.877188, -39.87773 , -39.878272, -39.878814, -39.879357, -39.879899,
       -39.880441, -39.880983, -39.881526, -39.882068, -39.88261 , -39.883152,
       -39.883695, -39.884237, -39.884779, -39.885321, -39.885863, -39.886406,
       -39.886948, -39.88749 , -39.888032, -39.888575, -39.889117, -39.889659,
       -39.890201, -39.890744, -39.891286, -39.891828, -39.89237 , -39.892913,
       -39.893455, -39.893997, -39.894539, -39.895081, -39.895624, -39.896166,
       -39.896708, -39.89725 , -39.897793, -39.898335, -39.898877, -39.899419,
       -39.899962, -39.900504, -39.901046, -39.901588, -39.90213 , -39.902673,
       -39.903215, -39.903757, -39.904299, -39.904842, -39.905384, -39.905926,
       -39.906468, -39.907011, -39.907553, -39.908095, -39.908637, -39.909179,
       -39.909722, -39.910264, -39.910806, -39.911348, -39.911891, -39.912433,
       -39.912975, -39.913517, -39.91406 , -39.914602, -39.915144, -39.915686,
       -39.916229, -39.916771, -39.917313, -39.917855, -39.918397, -39.91894 ,
       -39.919482, -39.920024, -39.920566, -39.921109, -39.921651, -39.922193,
       -39.922735, -39.923278, -39.92382 , -39.924362, -39.924904, -39.925446,
       -39.925989, -39.926531, -39.927073, -39.927615, -39.928158, -39.9287  ,
       -39.929242, -39.929784, -39.930327, -39.930869, -39.931411, -39.931953,
       -39.932495, -39.933038, -39.93358 , -39.934122, -39.934664, -39.935207,
       -39.935749, -39.936291, -39.936833, -39.937376, -39.937918, -39.93846 ,
       -39.939002, -39.939544, -39.940087, -39.940629, -39.941171, -39.941713,
       -39.942256, -39.942798, -39.94334 , -39.943882, -39.944425, -39.944967,
       -39.945509, -39.946051, -39.946594, -39.947136, -39.947678, -39.94822 ,
       -39.948762, -39.949305, -39.949847, -39.950389, -39.950931, -39.951474,
       -39.952016, -39.952558])
    • longitude
      (longitude)
      float64
      -62.2 -62.2 -62.2 ... -62.12 -62.12
      long_name :
      longitude
      units :
      degrees_east
      axis :
      X
      standard_name :
      longitude
      array([-62.204106, -62.203564, -62.203022, -62.20248 , -62.201938, -62.201395,
       -62.200853, -62.200311, -62.199769, -62.199226, -62.198684, -62.198142,
       -62.1976  , -62.197057, -62.196515, -62.195973, -62.195431, -62.194889,
       -62.194346, -62.193804, -62.193262, -62.19272 , -62.192177, -62.191635,
       -62.191093, -62.190551, -62.190008, -62.189466, -62.188924, -62.188382,
       -62.187839, -62.187297, -62.186755, -62.186213, -62.185671, -62.185128,
       -62.184586, -62.184044, -62.183502, -62.182959, -62.182417, -62.181875,
       -62.181333, -62.18079 , -62.180248, -62.179706, -62.179164, -62.178622,
       -62.178079, -62.177537, -62.176995, -62.176453, -62.17591 , -62.175368,
       -62.174826, -62.174284, -62.173741, -62.173199, -62.172657, -62.172115,
       -62.171573, -62.17103 , -62.170488, -62.169946, -62.169404, -62.168861,
       -62.168319, -62.167777, -62.167235, -62.166692, -62.16615 , -62.165608,
       -62.165066, -62.164523, -62.163981, -62.163439, -62.162897, -62.162355,
       -62.161812, -62.16127 , -62.160728, -62.160186, -62.159643, -62.159101,
       -62.158559, -62.158017, -62.157474, -62.156932, -62.15639 , -62.155848,
       -62.155306, -62.154763, -62.154221, -62.153679, -62.153137, -62.152594,
       -62.152052, -62.15151 , -62.150968, -62.150425, -62.149883, -62.149341,
       -62.148799, -62.148257, -62.147714, -62.147172, -62.14663 , -62.146088,
       -62.145545, -62.145003, -62.144461, -62.143919, -62.143376, -62.142834,
       -62.142292, -62.14175 , -62.141207, -62.140665, -62.140123, -62.139581,
       -62.139039, -62.138496, -62.137954, -62.137412, -62.13687 , -62.136327,
       -62.135785, -62.135243, -62.134701, -62.134158, -62.133616, -62.133074,
       -62.132532, -62.13199 , -62.131447, -62.130905, -62.130363, -62.129821,
       -62.129278, -62.128736, -62.128194, -62.127652, -62.127109, -62.126567,
       -62.126025, -62.125483, -62.124941, -62.124398, -62.123856, -62.123314,
       -62.122772, -62.122229, -62.121687, -62.121145, -62.120603, -62.12006 ,
       -62.119518, -62.118976, -62.118434, -62.117891, -62.117349, -62.116807,
       -62.116265])
    • wavelengths
      (bands)
      float32
      381.0 388.4 ... 2.486e+03 2.493e+03
      long_name :
      Wavelength Centers
      units :
      nm
      array([ 381.00558,  388.4092 ,  395.81583,  403.2254 ,  410.638  ,
        418.0536 ,  425.47214,  432.8927 ,  440.31726,  447.7428 ,
        455.17035,  462.59888,  470.0304 ,  477.46292,  484.89743,
        492.33292,  499.77142,  507.2099 ,  514.6504 ,  522.0909 ,
        529.5333 ,  536.9768 ,  544.42126,  551.8667 ,  559.3142 ,
        566.7616 ,  574.20905,  581.6585 ,  589.108  ,  596.55835,
        604.0098 ,  611.4622 ,  618.9146 ,  626.36804,  633.8215 ,
        641.2759 ,  648.7303 ,  656.1857 ,  663.6411 ,  671.09753,
        678.5539 ,  686.0103 ,  693.4677 ,  700.9251 ,  708.38354,
        715.84094,  723.2993 ,  730.7587 ,  738.2171 ,  745.6765 ,
        753.1359 ,  760.5963 ,  768.0557 ,  775.5161 ,  782.97754,
        790.4379 ,  797.89935,  805.36176,  812.8232 ,  820.2846 ,
        827.746  ,  835.2074 ,  842.66986,  850.1313 ,  857.5937 ,
        865.0551 ,  872.5176 ,  879.98004,  887.44147,  894.90393,
        902.3664 ,  909.82886,  917.2913 ,  924.7538 ,  932.21625,
        939.6788 ,  947.14026,  954.6027 ,  962.0643 ,  969.5268 ,
        976.9883 ,  984.4498 ,  991.9114 ,  999.37286, 1006.8344 ,
       1014.295  , 1021.7566 , 1029.2172 , 1036.6777 , 1044.1383 ,
       1051.5989 , 1059.0596 , 1066.5201 , 1073.9797 , 1081.4404 ,
       1088.9    , 1096.3597 , 1103.8184 , 1111.2781 , 1118.7368 ,
...
       1796.4385 , 1803.8701 , 1811.3008 , 1818.7314 , 1826.1611 ,
       1833.591  , 1841.0206 , 1848.4495 , 1855.8773 , 1863.3052 ,
       1870.733  , 1878.16   , 1885.5869 , 1893.013  , 1900.439  ,
       1907.864  , 1915.2892 , 1922.7133 , 1930.1375 , 1937.5607 ,
       1944.9839 , 1952.4071 , 1959.8295 , 1967.2518 , 1974.6732 ,
       1982.0946 , 1989.515  , 1996.9355 , 2004.355  , 2011.7745 ,
       2019.1931 , 2026.6118 , 2034.0304 , 2041.4471 , 2048.865  ,
       2056.2808 , 2063.6965 , 2071.1123 , 2078.5273 , 2085.9421 ,
       2093.3562 , 2100.769  , 2108.1821 , 2115.5942 , 2123.0063 ,
       2130.4175 , 2137.8289 , 2145.239  , 2152.6482 , 2160.0576 ,
       2167.467  , 2174.8755 , 2182.283  , 2189.6904 , 2197.097  ,
       2204.5034 , 2211.9092 , 2219.3147 , 2226.7195 , 2234.1233 ,
       2241.5269 , 2248.9297 , 2256.3328 , 2263.7346 , 2271.1365 ,
       2278.5376 , 2285.9387 , 2293.3386 , 2300.7378 , 2308.136  ,
       2315.5342 , 2322.9326 , 2330.3298 , 2337.7263 , 2345.1216 ,
       2352.517  , 2359.9126 , 2367.3071 , 2374.7007 , 2382.0935 ,
       2389.486  , 2396.878  , 2404.2695 , 2411.6604 , 2419.0513 ,
       2426.4402 , 2433.8303 , 2441.2183 , 2448.6064 , 2455.9944 ,
       2463.3816 , 2470.7678 , 2478.153  , 2485.5386 , 2492.9238 ],
      dtype=float32)
    • fwhm
      (bands)
      float32
      8.415 8.415 8.415 ... 8.807 8.809
      long_name :
      Full Width at Half Max
      units :
      nm
      array([8.415, 8.415, 8.415, 8.415, 8.417, 8.418, 8.419, 8.421, 8.422,
       8.424, 8.425, 8.426, 8.428, 8.429, 8.431, 8.432, 8.433, 8.435,
       8.436, 8.438, 8.439, 8.44 , 8.442, 8.443, 8.445, 8.446, 8.447,
       8.449, 8.45 , 8.452, 8.453, 8.454, 8.456, 8.457, 8.459, 8.46 ,
       8.461, 8.463, 8.464, 8.466, 8.467, 8.468, 8.47 , 8.471, 8.473,
       8.474, 8.475, 8.477, 8.478, 8.48 , 8.481, 8.482, 8.484, 8.485,
       8.487, 8.488, 8.489, 8.491, 8.492, 8.494, 8.495, 8.496, 8.498,
       8.499, 8.501, 8.502, 8.503, 8.505, 8.506, 8.508, 8.509, 8.51 ,
       8.512, 8.513, 8.515, 8.516, 8.517, 8.519, 8.52 , 8.522, 8.523,
       8.524, 8.526, 8.527, 8.529, 8.53 , 8.531, 8.533, 8.534, 8.536,
       8.537, 8.538, 8.54 , 8.541, 8.543, 8.544, 8.545, 8.547, 8.548,
       8.55 , 8.551, 8.552, 8.554, 8.555, 8.557, 8.558, 8.559, 8.561,
       8.562, 8.564, 8.565, 8.566, 8.568, 8.569, 8.571, 8.572, 8.573,
       8.575, 8.576, 8.578, 8.579, 8.58 , 8.582, 8.583, 8.585, 8.586,
       8.587, 8.589, 8.59 , 8.592, 8.593, 8.594, 8.596, 8.597, 8.599,
       8.6  , 8.601, 8.603, 8.604, 8.606, 8.607, 8.608, 8.61 , 8.611,
       8.613, 8.614, 8.615, 8.617, 8.618, 8.62 , 8.621, 8.622, 8.624,
       8.625, 8.627, 8.628, 8.629, 8.631, 8.632, 8.634, 8.635, 8.636,
       8.638, 8.639, 8.641, 8.642, 8.643, 8.645, 8.646, 8.648, 8.649,
       8.65 , 8.652, 8.653, 8.655, 8.656, 8.657, 8.659, 8.66 , 8.662,
       8.663, 8.664, 8.666, 8.667, 8.669, 8.67 , 8.671, 8.673, 8.674,
       8.676, 8.677, 8.678, 8.68 , 8.681, 8.683, 8.684, 8.685, 8.687,
       8.688, 8.69 , 8.691, 8.692, 8.694, 8.695, 8.697, 8.698, 8.699,
       8.701, 8.702, 8.704, 8.705, 8.706, 8.708, 8.709, 8.711, 8.712,
       8.714, 8.715, 8.716, 8.718, 8.719, 8.721, 8.722, 8.723, 8.725,
       8.726, 8.727, 8.729, 8.73 , 8.732, 8.733, 8.734, 8.736, 8.737,
       8.739, 8.74 , 8.741, 8.743, 8.744, 8.746, 8.747, 8.748, 8.75 ,
       8.751, 8.753, 8.754, 8.755, 8.757, 8.758, 8.76 , 8.761, 8.763,
       8.764, 8.765, 8.767, 8.768, 8.77 , 8.771, 8.772, 8.774, 8.775,
       8.777, 8.778, 8.779, 8.781, 8.782, 8.783, 8.785, 8.786, 8.788,
       8.789, 8.79 , 8.792, 8.793, 8.795, 8.796, 8.797, 8.799, 8.8  ,
       8.802, 8.803, 8.804, 8.806, 8.807, 8.809], dtype=float32)
    • spatial_ref
      ()
      int32
      0
      crs_wkt :
      GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
      semi_major_axis :
      6378137.0
      semi_minor_axis :
      6356752.314245179
      inverse_flattening :
      298.257223563
      reference_ellipsoid_name :
      WGS 84
      longitude_of_prime_meridian :
      0.0
      prime_meridian_name :
      Greenwich
      geographic_crs_name :
      WGS 84
      grid_mapping_name :
      latitude_longitude
      spatial_ref :
      GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
      GeoTransform :
      -62.20437757755081 0.0005422325202563399 0.0 -39.87691664255127 0.0 -0.0005422325202563658
      array(0)
    • reflectance
      (latitude, longitude, bands)
      float32
      nan nan nan nan ... nan nan nan nan
      long_name :
      Surface Reflectance
      units :
      unitless
      array([[[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
...
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]],

       [[nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        ...,
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan],
        [nan, nan, nan, ..., nan, nan, nan]]], dtype=float32)
    • latitude
      PandasIndex
      PandasIndex(Float64Index([  -39.8771877588114, -39.877729991331655,  -39.87827222385191,
               -39.87881445637217,  -39.87935668889242,  -39.87989892141268,
              -39.880441153932935, -39.880983386453195,  -39.88152561897345,
               -39.88206785149371,
              ...
              -39.947677986444724, -39.948220218964984,  -39.94876245148524,
                -39.9493046840055,  -39.94984691652575,  -39.95038914904601,
              -39.950931381566264, -39.951473614086524,  -39.95201584660678,
               -39.95255807912704],
             dtype='float64', name='latitude', length=140))
    • longitude
      PandasIndex
      PandasIndex(Float64Index([ -62.20410646129068, -62.203564228770425, -62.203021996250165,
               -62.20247976372991,  -62.20193753120966,   -62.2013952986894,
              -62.200853066169145, -62.200310833648885,  -62.19976860112863,
               -62.19922636860837,
              ...
               -62.12114488569146,   -62.1206026531712, -62.120060420650944,
               -62.11951818813069,  -62.11897595561043,  -62.11843372309018,
               -62.11789149056992, -62.117349258049664, -62.116807025529404,
               -62.11626479300915],
             dtype='float64', name='longitude', length=163))
  • ncei_template_version :
    NCEI_NetCDF_Swath_Template_v2.0
    summary :
    The Earth Surface Mineral Dust Source Investigation (EMIT) is an Earth Ventures-Instrument (EVI-4) Mission that maps the surface mineralogy of arid dust source regions via imaging spectroscopy in the visible and short-wave infrared (VSWIR). Installed on the International Space Station (ISS), the EMIT instrument is a Dyson imaging spectrometer that uses contiguous spectroscopic measurements from 410 to 2450 nm to resolve absoprtion features of iron oxides, clays, sulfates, carbonates, and other dust-forming minerals. During its one-year mission, EMIT will observe the sunlit Earth's dust source regions that occur within +/-52° latitude and produce maps of the source regions that can be used to improve forecasts of the role of mineral dust in the radiative forcing (warming or cooling) of the atmosphere.\n\nThis file contains L2A estimated surface reflectances and geolocation data. Reflectance estimates are created using an Optimal Estimation technique - see ATBD for details. Reflectance values are reported as fractions (relative to 1).
    keywords :
    Imaging Spectroscopy, minerals, EMIT, dust, radiative forcing
    Conventions :
    CF-1.63
    sensor :
    EMIT (Earth Surface Mineral Dust Source Investigation)
    instrument :
    EMIT
    platform :
    ISS
    processing_version :
    V1.0
    institution :
    NASA Jet Propulsion Laboratory/California Institute of Technology
    license :
    https://science.nasa.gov/earth-science/earth-science-data/data-information-policy/
    naming_authority :
    LPDAAC
    date_created :
    2022-11-14T09:50:54Z
    keywords_vocabulary :
    NASA Global Change Master Directory (GCMD) Science Keywords
    stdname_vocabulary :
    NetCDF Climate and Forecast (CF) Metadata Convention
    creator_name :
    Jet Propulsion Laboratory/California Institute of Technology
    creator_email :
    sarah.r.lundeen@jpl.nasa.gov
    creator_url :
    https://earth.jpl.nasa.gov/emit/
    project :
    Earth Surface Mineral Dust Source Investigation
    project_url :
    https://emit.jpl.nasa.gov/
    publisher_name :
    USGS LPDAAC
    publisher_url :
    https://lpdaac.usgs.gov
    publisher_email :
    lpdaac@usgs.gov
    identifier_product_doi_authority :
    https://doi.org
    flight_line :
    emit20220903t163129_o24611_s000
    time_coverage_start :
    2022-09-03T16:31:29+0000
    time_coverage_end :
    2022-09-03T16:31:41+0000
    software_build_version :
    010603
    product_version :
    01
    history :
    PGE Input files: radiance_file=/beegfs/store/emit/ops/data/acquisitions/20220903/emit20220903t163129/l1b/emit20220903t163129_o24611_s000_l1b_rdn_b0106_v01.img, pixel_locations_file=/beegfs/store/emit/ops/data/acquisitions/20220903/emit20220903t163129/l1b/emit20220903t163129_o24611_s000_l1b_loc_b0106_v01.img, observation_parameters_file=/beegfs/store/emit/ops/data/acquisitions/20220903/emit20220903t163129/l1b/emit20220903t163129_o24611_s000_l1b_obs_b0106_v01.img, surface_model_config=/beegfs/store/emit/ops/repos/emit-sds-l2a/surface/surface_20221020.json
    easternmost_longitude :
    -62.5120945327963
    northernmost_latitude :
    -39.3067591475017
    westernmost_longitude :
    -61.236221412633064
    southernmost_latitude :
    -40.39610428069674
    spatialResolution :
    0.000542232520256367
    spatial_ref :
    GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AXIS["Latitude",NORTH],AXIS["Longitude",EAST],AUTHORITY["EPSG","4326"]]
    geotransform :
    [-6.25120945e+01 5.42232520e-04 -0.00000000e+00 -3.93067591e+01 -0.00000000e+00 -5.42232520e-04]
    day_night_flag :
    Day
    title :
    EMIT L2A Surface Reflectance 60 m V001

Select a band from the clipped dataset and plot it spatially.

In [7]:
clipped.isel(bands=20).hvplot.image(cmap='viridis', aspect = 'equal', frame_width=500, rasterize=True)
Out[7]:

Now we can save the clipped xarray.Dataset as a netCDF4 output that can be reopened using the xarray.open_dataset function.

In [ ]:
clipped.to_netcdf('../data/clipped_data.nc')
# Example for Opening 
# ds = xr.open_dataset('../data/clipped_data.nc')

Contact Info:¶

Email: LPDAAC@usgs.gov
Voice: +1-866-573-3222
Organization: Land Processes Distributed Active Archive Center (LP DAAC)¹
Website: https://lpdaac.usgs.gov/
Date last modified: 01-04-2023

¹Work performed under USGS contract G15PD00467 for NASA contract NNG14HH33I.